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Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of similar to 35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.

Oaks (Quercus: Fagaceae) commonly interbreed yet retain their morphological, genetic and ecological distinctiveness. Post-zygotic isolation mechanisms, such as ecologically dependent selection on adaptive loci, may therefore limit introgression. To test this hypothesis, we quantified hybridization and genetic divergence across the contact zone of four red oaks (Quercus section Lobatae) in the Great Lakes region of North America using a suite of 259 amplified fragment length polymorphisms and 27 genic and genomic microsatellite markers. First, we identified hybrids using genetic structure analysis and confirmed the reliability of our assignments via simulations. Then, we identified candidate loci for species maintenance with three complementary tests for selection and obtained partial gene sequences linked to an outlier locus and three other loci. We detected evidence of recent hybridization among all species and considerable gene flow between Q.ellipsoidalis and Q.velutina. Overall, c.20% of Q.velutina had recent ancestry from Q.ellipsoidalis, whereas nearly 30% of Q.ellipsoidalis had a Q.velutina ancestor. Most loci were negligibly to weakly differentiated among species, but two gene-linked microsatellites deviated significantly from neutral expectations in multiple, complementary outlier tests. Both outlier loci were located in the same 15-cM bin on an existing Q.robur linkage map, a region under divergent selection in other oak species. Adaptive loci in this highly differentiated genomic region may contribute to ecological divergence among species and limit introgression.

Many birds have advanced their spring migration and breeding phenology in response to climate change, yet some long-distance migrants appear constrained in their adjustments. In addition, bird species with long generation times and those in higher trophic positions may also be less able to track climate-induced shifts in food availability. Migratory birds of prey may therefore be particularly vulnerable to climate change because: 1) most are long-lived and have relatively low reproductive capacity, 2) many feed predominately on insectivorous passerines, and 3) several undertake annual migrations totaling tens of thousands of kilometers. Using multi-decadal datasets for 14 raptor species observed at six sites across the Great Lakes region of North America, we detected phenological shifts in spring migration consistent with decadal climatic oscillations and global climate change. While the North Atlantic and El Nino Southern Oscillations exerted heterogeneous effects on the phenology of a few species, arrival dates more generally advanced by 1.18 d per decade, a pattern consistent with the effects of global climate change. After accounting for heterogeneity across observation sites, five of the 10 most abundant species advanced the bulk of their spring migration phenology. Contrary to expectations, we found that long-distance migrants and birds with longer generation times tended to make the greatest advancements to their spring migration. Such results may indicate that phenotypic plasticity can facilitate climatic responses among these long-lived predators.